Whether or not this happens is purely conjecture at this point, but there is a strong possibility that apparently, the Windows machines that have been used the the North Koreans may very well overwrite import parts of the disk.
The plus side is that the malware they used, MyDoom, has been around since 2004 (according to the article). If nothing else, that should limit the number of attack vectors out there.
Edit: The original report claimed that all attached hard drives would be overwritten. South Korean researchers claim that only the first 1024 bytes of the boot disk are overwritten. While this would render the machine unbootable, any other devices should be okay.